From 4839fdb76fe72e556646b5a1bdf10f582683d4b3 Mon Sep 17 00:00:00 2001
From: Lingyun Zhao <33519183+lingyun1010@users.noreply.github.com>
Date: Wed, 4 Oct 2023 18:35:15 +0100
Subject: [PATCH] Add url decoder for cell type heatmap search (#355)

* Add url decoder for cell type heatmap search

* Cover the case when cell type contains a forward slash

* Fix the test for checking the empty payload

and improve the naming of the test methods

---------

Co-authored-by: Karoly Erdos <karoly@ebi.ac.uk>
---
 ...perimentCellTypeMarkerGenesController.java |  8 ++++--
 ...imentCellTypeMarkerGenesControllerWIT.java | 28 ++++++++++++++++---
 2 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/app/src/main/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesController.java b/app/src/main/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesController.java
index a035c6eef..9d6668c0c 100644
--- a/app/src/main/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesController.java
+++ b/app/src/main/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesController.java
@@ -9,6 +9,8 @@
 import uk.ac.ebi.atlas.controllers.JsonExceptionHandlingController;
 import uk.ac.ebi.atlas.experimentpage.markergenes.HighchartsHeatmapAdapter;
 
+import java.net.URLDecoder;
+import java.nio.charset.StandardCharsets;
 import java.util.Collection;
 
 import static uk.ac.ebi.atlas.utils.GsonProvider.GSON;
@@ -33,8 +35,10 @@ public String getCellTypeMarkerGenes(
         return GSON.toJson(
                 highchartsHeatmapAdapter.getMarkerGeneHeatmapDataSortedLexicographically(
                         experimentAccessions == null ?
-                                multiexperimentCellTypeMarkerGenesService.getCellTypeMarkerGeneProfile(cellType) :
                                 multiexperimentCellTypeMarkerGenesService.getCellTypeMarkerGeneProfile(
-                                        ImmutableSet.copyOf(experimentAccessions), cellType)));
+                                        URLDecoder.decode(cellType, StandardCharsets.UTF_8)) :
+                                multiexperimentCellTypeMarkerGenesService.getCellTypeMarkerGeneProfile(
+                                        ImmutableSet.copyOf(experimentAccessions),
+                                        URLDecoder.decode(cellType, StandardCharsets.UTF_8))));
     }
 }
diff --git a/app/src/test/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesControllerWIT.java b/app/src/test/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesControllerWIT.java
index 43a25adfe..a3017db7a 100644
--- a/app/src/test/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesControllerWIT.java
+++ b/app/src/test/java/uk/ac/ebi/atlas/search/metadata/JsonMultiexperimentCellTypeMarkerGenesControllerWIT.java
@@ -14,6 +14,11 @@
 import org.springframework.web.context.WebApplicationContext;
 import uk.ac.ebi.atlas.configuration.TestConfig;
 
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+
+import static org.hamcrest.Matchers.empty;
+import static org.hamcrest.Matchers.is;
 import static org.hamcrest.Matchers.isA;
 import static org.springframework.test.context.jdbc.Sql.ExecutionPhase.AFTER_TEST_METHOD;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
@@ -56,9 +61,22 @@ void setUp() {
     }
 
     @Test
-    void returnsAValidJsonPayloadForAValidCellType() throws Exception {
+    void shouldReturnAValidJsonPayloadForAValidCellType() throws Exception {
         this.mockMvc.perform(get("/json/cell-type-marker-genes/{cellType}", "cell cycle S phase")
-                .param("experimentAccession", "E-ENAD-53"))
+                        .param("experimentAccession", "E-ENAD-53"))
+                .andExpect(status().isOk())
+                .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+                .andExpect(jsonPath("$[0].cellGroupValue", isA(String.class)))
+                .andExpect(jsonPath("$[0].value", isA(Number.class)))
+                .andExpect(jsonPath("$[0].cellGroupValueWhereMarker", isA(String.class)))
+                .andExpect(jsonPath("$[0].pValue", isA(Number.class)));
+    }
+
+    @Test
+    void shouldReturnAValidJsonPayloadForACellTypeContainingAForwardSlash() throws Exception {
+        final String encodedCellType = URLEncoder.encode("cell cycle G2/M phase", StandardCharsets.UTF_8);
+        this.mockMvc.perform(get("/json/cell-type-marker-genes/{cellType}", encodedCellType)
+                        .param("experimentAccession", "E-ENAD-53"))
                 .andExpect(status().isOk())
                 .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
                 .andExpect(jsonPath("$[0].cellGroupValue", isA(String.class)))
@@ -68,9 +86,11 @@ void returnsAValidJsonPayloadForAValidCellType() throws Exception {
     }
 
     @Test
-    void returnsEmptyPayloadForAnInvalidCellType() throws Exception {
+    void shouldReturnEmptyPayloadForAnInvalidCellType() throws Exception {
         this.mockMvc.perform(get("/json/cell-type-marker-genes/{cellType}", "fooBar")
                 .param("experimentAccession", "E-CURD-4"))
-                .andExpect(status().isOk());
+                .andExpect(status().isOk())
+                .andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+                .andExpect(jsonPath("$", is(empty())));
     }
 }